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Yorodumi- PDB-5lt5: Carboxysome shell protein CcmP from Synechococcus elongatus PCC 7942 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lt5 | |||||||||||||||
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Title | Carboxysome shell protein CcmP from Synechococcus elongatus PCC 7942 | |||||||||||||||
Components | CcmP | |||||||||||||||
Keywords | TRANSPORT PROTEIN / Carboxysome Shell protein BMC domain Gated transport | |||||||||||||||
Function / homology | Function and homology information structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis Similarity search - Function | |||||||||||||||
Biological species | Synechococcus elongatus PCC 7942 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | |||||||||||||||
Authors | Larsson, A.M. / Hasse, D. / Valegard, K. / Andersson, I. | |||||||||||||||
Funding support | Sweden, 4items
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Citation | Journal: J. Exp. Bot. / Year: 2017 Title: Crystal structures of beta-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore. Authors: Larsson, A.M. / Hasse, D. / Valegard, K. / Andersson, I. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lt5.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lt5.ent.gz | 140 KB | Display | PDB format |
PDBx/mmJSON format | 5lt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lt5_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 5lt5_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | 5lt5_validation.xml.gz | 19 KB | Display | |
Data in CIF | 5lt5_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/5lt5 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/5lt5 | HTTPS FTP |
-Related structure data
Related structure data | 5lsrC 4ht5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24271.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria) Gene: Synpcc7942_0520 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q31QW7 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mM BIS-tris propane, 50 mM NaCl, 10 mM glycerol, 0.2 M Li sulphate, 0.1 mM Tris-HCl pH 7.5 and 5% w/v PEG 4000, 50 mM RuBP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2014 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.45→47.92 Å / Num. obs: 72625 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 19.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.7 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HT5 Resolution: 1.45→47.92 Å / Cor.coef. Fo:Fc: 0.9615 / Cor.coef. Fo:Fc free: 0.9536 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.061 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.059
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Displacement parameters | Biso max: 101.51 Å2 / Biso mean: 21.32 Å2 / Biso min: 11.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.145 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→47.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.49 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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